miRNA: 3'- -UUUAGGaggUAACGGU-GGGCCGAGCU- -5'
miRNA: 3'- -UUUAGg-AGGUaaCGG---UGGGCCGAGCU- -5'
miRNA: 3'- uuuAGGAGGUAACGGUGGgccGaGCU- -5'
miRNA: 3'- -UUUAGGA---------GGU-----------AACGG------UGGGCCGAGCU- -5'
miRNA: 3'- -UUUAGGAGGUAACGGUGGGCCGAGCU- -5'
Results 1 - 5 of 5 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 16653 | 3' | -55.7 | NC_004156.1 | + | 214176 | 0.67 | 0.929603 |
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Target: 5'- cAGAUUCagaGUUGCCGuCUCGGCUCGGu -3' miRNA: 3'- -UUUAGGaggUAACGGU-GGGCCGAGCU- -5' |
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| 16653 | 3' | -55.7 | NC_004156.1 | + | 169873 | 0.67 | 0.92435 |
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Target: 5'- gAAAUCaaUCUAgaGCCacuGCCCGGCUUGAg -3' miRNA: 3'- -UUUAGg-AGGUaaCGG---UGGGCCGAGCU- -5' |
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| 16653 | 3' | -55.7 | NC_004156.1 | + | 41007 | 0.68 | 0.881123 |
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Target: 5'- --cUCCUCCAUUGCCGCCa--C-CGAa -3' miRNA: 3'- uuuAGGAGGUAACGGUGGgccGaGCU- -5' |
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| 16653 | 3' | -55.7 | NC_004156.1 | + | 77044 | 0.7 | 0.801651 |
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Target: 5'- gGGAUCCUcacacgagcCCAgcagacccagaUUGCCcacguaGCCCGGCUCGGu -3' miRNA: 3'- -UUUAGGA---------GGU-----------AACGG------UGGGCCGAGCU- -5' |
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| 16653 | 3' | -55.7 | NC_004156.1 | + | 170169 | 1.06 | 0.006419 |
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Target: 5'- uAAAUCCUCCAUUGCCACCCGGCUCGAc -3' miRNA: 3'- -UUUAGGAGGUAACGGUGGGCCGAGCU- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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